Executable : siesta Version : 5.4.2 Architecture : x86_64 Compiler version: GNU-14.3.0 Compiler flags : -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /include -I/_build_env/include -fdebug-prefix-map=/work=/usr/local/src/conda/siesta-5.4.2 -fdebug-prefix-map==/usr/local/src/conda-prefix -I/lib -fallow-argument-mismatch -O3 Parallelisations: none NetCDF support NetCDF-4 support Lua support DFT-D3 support Runtime information: * Directory : /home/apolyukhin/Development/HPRO/examples/Diamond/aobasis * Running in serial mode. >> Start of run: 31-JAN-2026 22:37:41 *********************** * WELCOME TO SIESTA * *********************** NOTE: Siesta V5 introduces some new defaults for basis-set generation NOTE: which might lead to slightly different numerical results. NOTE: Please see the manual for full details and compatibility measures. reinit: Reading from standard input reinit: Dumping input in INPUT_TMP.08556 ************************** Dump of input data file **************************** SystemName Diamond SystemLabel siesta NumberOfAtoms 2 NumberOfSpecies 1 %block ChemicalSpeciesLabel 1 6 C %endblock ChemicalSpeciesLabel LatticeConstant 3.567 Ang %block LatticeVectors 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 %endblock LatticeVectors AtomicCoordinatesFormat Fractional %block AtomicCoordinatesAndAtomicSpecies 0.00 0.00 0.00 1 0.25 0.25 0.25 1 %endblock AtomicCoordinatesAndAtomicSpecies PAO.BasisSize DZP PAO.BasisType nodes %block PAO.Basis C 2 n=2 0 2 0.000 0.000 1.000 1.000 n=2 1 2 P 0.000 0.000 1.000 1.000 %endblock PAO.Basis %block kgrid_Monkhorst_Pack 4 0 0 0.0 0 4 0 0.0 0 0 4 0.0 %endblock kgrid_Monkhorst_Pack SolutionMethod diagon OccupationFunction MP ElectronicTemperature 0.0000 eV MaxSCFIterations 300 MeshCutoff 320.0 Ry DM.Tolerance 1.E-6 SCF.H.Converge F UseSaveData F DM.UseSaveDM F SpinOrbit F Diag.ParallelOverK T ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: Diamond reinit: ----------------------------------------------------------------------- reinit: System Label: siesta reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- Species number: 1 Atomic number: 6 Label: C Ground state valence configuration (from tables): 2s02 2p02 3d00 4f00 ---- Processing specs for species: C Reading pseudopotential information in PSML from: C.psml PSML file version: 1.1 Using libxc ids: 101 130 GGA--PBE XC_GGA_X_PBE--XC_GGA_C_PBE pb PSML uuid: 297821e0-be41-11e7-6802-e1ff7dfff095 ---- Pseudopotential check for C Pseudized shells: 2s( 2.00) rc: 1.20 2p( 2.00) rc: 1.26 Valence configuration for ps generation: 2s:2p: Total charge: 4.000000 C: adding empty (pol) shell: 3d For C, standard SIESTA heuristics set lmxkb to 3 (one more than the basis l, including polarization orbitals). Use PS.lmax or PS.KBprojectors blocks to override. C pseudopotential only contains V_ls up to l=1 -- lmxkb reset. =============================================================================== C Z= 6 Mass= 12.011 Charge= 0.17977+309 Lmxo=2 Lmxkb= 1 BasisType=nodes Semic=F L=0 Nsemic=0 Cnfigmx=2 i=1 nzeta=2 polorb=0 (2s) splnorm: 0.15000 vcte: 40.000 rinn: -0.90000 qcoe: 0.0000 qyuk: 0.0000 qwid: 0.10000E-01 rcs: 0.0000 0.0000 lambdas: 1.0000 1.0000 L=1 Nsemic=0 Cnfigmx=2 i=1 nzeta=2 polorb=1 (2p) (to be polarized perturbatively) splnorm: 0.15000 vcte: 40.000 rinn: -0.90000 qcoe: 0.0000 qyuk: 0.0000 qwid: 0.10000E-01 rcs: 0.0000 0.0000 lambdas: 1.0000 1.0000 L=2 Nsemic=0 Cnfigmx=3 i=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital) (from 2p) ------------------------------------------------------------------------------- L=0 Nkbl=1 erefs: 0.17977+309 L=1 Nkbl=1 erefs: 0.17977+309 =============================================================================== Using PAO.SplitTailNorm atom: Called for C (Z = 6) NOTE: C pseudopotential has channels up to l= 1 NOTE: PAOs with higher l will be generated with V_local Maximum radius (at nrval) set to 50.00000 8518 read_vps: Pseudopotential generation method: read_vps: ONCVPSP-3.Hamann's oncvpsp Valence charge in pseudo generation: 4.00000 read_vps: Pseudopotential includes a core correction: read_vps: Pseudo-core for xc-correction xc_check: Exchange-correlation functional: xc_check: Ceperley-Alder xc_check: WARNING: Pseudopotential generated with GGA PBE functional Got Vlocal (oncv-fit) from psml data Choosing vlocal chloc cutoff: 4.122282 qtot up to nchloc: 4.00001153 atom: Maximum radius for chlocal: 4.12228 atom: Maximum radius for r*vlocal+2*Zval: 4.12228 Reading KB projs from C psml data Using scalar-relativistic projectors in PSML file PSML: Kleinman-Bylander projectors: l= 0 rc= 1.219773 Ekb= 12.963096 l= 0 rc= 1.219773 Ekb= 0.771007 l= 1 rc= 1.278952 Ekb= -8.399923 l= 1 rc= 1.278952 Ekb= -1.755033 PSML: Total number of Kleinman-Bylander projectors: 8 atom: ------------------------------------------------------------------------- atom: SANKEY-TYPE ORBITALS: atom: Selected multiple-zeta basis: nodes NODES: Orbitals with angular momentum L= 0 NODES: Basis orbitals for state 2s NODES: PAO cut-off radius determinated from an NODES: energy shift= 0.010000 Ry izeta = 1 lambda = 1.000000 rc = 4.511437 energy = -0.990536 kinetic = 0.937580 potential(screened) = -1.928116 potential(ionic) = -5.484011 izeta = 2 lambda = 1.000000 rc = 4.511437 energy = 0.891142 kinetic = 1.793173 potential(screened) = -0.902030 potential(ionic) = -3.534576 NODES: Orbitals with angular momentum L= 1 NODES: Basis orbitals for state 2p NODES: PAO cut-off radius determinated from an NODES: energy shift= 0.010000 Ry izeta = 1 lambda = 1.000000 rc = 5.490449 energy = -0.370949 kinetic = 2.425333 potential(screened) = -2.796282 potential(ionic) = -6.202636 izeta = 2 lambda = 1.000000 rc = 5.490449 energy = 0.680157 kinetic = 2.141732 potential(screened) = -1.461575 potential(ionic) = -3.873772 *Note: V_local used for l= 2 ** Using vlocal for PAOs with L= 2 POLgen: Perturbative polarization orbital with L= 2 POLgen: Polarization orbital for state 2p *Note: V_local used for lpol= 2 ** Using vlocal for PAOs with L= 2 Split based on tail norm izeta = 1 rc = 5.490449 energy = 1.123484 kinetic = 2.219016 potential(screened) = -1.095531 potential(ionic) = -3.908003 atom: Total number of Sankey-type orbitals: 13 atm_pop: Valence configuration (for local Pseudopot. screening): 2s( 2.00) 2p( 2.00) 3d( 0.00) Vna: chval, zval: 4.00000 4.00000 Vna: Cut-off radius for the neutral-atom potential: 5.490449 comcore: Pseudo-core radius Rcore= 1.671741 atom: _________________________________________________________________________ prinput: Basis input PAO.BasisType nodes %block ChemicalSpeciesLabel 1 6 C # Species index, atomic number, species label %endblock ChemicalSpeciesLabel %block PAO.Basis # Define Basis set # WARNING: This information might be incomplete! C 2 # Species label, number of l-shells n=2 0 2 # n, l, Nzeta 4.511 4.511 1.000 1.000 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 5.490 5.490 1.000 1.000 %endblock PAO.Basis prinput: ---------------------------------------------------------------------- Dumping basis to NetCDF file C.ion.nc coor: Atomic-coordinates input format = Fractional siesta: Atomic coordinates (Bohr) and species siesta: 0.00000 0.00000 0.00000 1 1 siesta: 1.68516 1.68516 1.68516 1 2 siesta: System type = bulk initatomlists: Number of atoms, orbitals, and projectors: 2 26 16 siesta: ******************** Simulation parameters **************************** siesta: siesta: The following are some of the parameters of the simulation. siesta: A complete list of the parameters used, including default values, siesta: can be found in file out.fdf siesta: redata: Spin configuration = none redata: Number of spin components = 1 redata: Time-Reversal Symmetry = T redata: Spin spiral = F redata: Long output = F redata: Number of Atomic Species = 1 redata: Charge density info will appear in .RHO file redata: Write Mulliken charges (when) = none redata: Write Mulliken Pop. = NO redata: Write Hirshfeld charges (when) = none redata: Write Voronoi charges (when) = none redata: Write spin charge (when) = none redata: Matel table size (NRTAB) = 1024 redata: Mesh Cutoff = 320.0000 Ry redata: Net charge of the system = 0.0000 |e| redata: Min. number of SCF Iter = 0 redata: Max. number of SCF Iter = 300 redata: SCF convergence failure will abort job redata: SCF mix quantity = Hamiltonian redata: Mix DM or H after convergence = F redata: Recompute H after scf cycle = F redata: Mix DM in first SCF step = T redata: Write Pulay info on disk = F redata: New DM Occupancy tolerance = 0.000000000001 redata: No kicks to SCF redata: DM Mixing Weight for Kicks = 0.5000 redata: Require Harris convergence for SCF = F redata: Harris energy tolerance for SCF = 0.000100 eV redata: Require DM convergence for SCF = T redata: DM tolerance for SCF = 0.000001 redata: Require EDM convergence for SCF = F redata: EDM tolerance for SCF = 0.001000 eV redata: Require H convergence for SCF = F redata: Hamiltonian tolerance for SCF = 0.001000 eV redata: Require (free) Energy convergence for SCF = F redata: (free) Energy tolerance for SCF = 0.000100 eV redata: Using DFT-D3 dispersion = F redata: Using Saved Data (generic) = F redata: Use continuation files for DM = F redata: Neglect nonoverlap interactions = F redata: Method of Calculation = Diagonalization redata: Electronic Temperature = 0.0000 K redata: Fix the spin of the system = F redata: Max. number of TDED Iter = 1 redata: Number of TDED substeps = 3 redata: Dynamics option = Single-point calculation mix.SCF: Pulay mixing = Pulay mix.SCF: Variant = stable mix.SCF: History steps = 2 mix.SCF: Linear mixing weight = 0.250000 mix.SCF: Mixing weight = 0.250000 mix.SCF: SVD condition = 0.1000E-07 redata: Save all siesta data in one NC = F redata: *********************************************************************** %block SCF.Mixers Pulay %endblock SCF.Mixers %block SCF.Mixer.Pulay # Mixing method method pulay variant stable # Mixing options weight 0.2500 weight.linear 0.2500 history 2 %endblock SCF.Mixer.Pulay DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation Size of DM history Fstack: 1 Total number of electrons: 8.000000 Total ionic charge: 8.000000 k-point displ. along 1 input, could be: 0.00 0.50 k-point displ. along 2 input, could be: 0.00 0.50 k-point displ. along 3 input, could be: 0.00 0.50 Kpoints in: 48 . Kpoints trimmed: 44 siesta: k-grid: Number of k-points = 44 siesta: k-points from Monkhorst-Pack grid siesta: k-cutoff (effective) = 5.044 Ang siesta: k-point supercell and displacements siesta: k-grid: 4 0 0 0.000 siesta: k-grid: 0 4 0 0.000 siesta: k-grid: 0 0 4 0.000 diag: Algorithm = D&C diag: Used triangular part = Lower diag: Absolute tolerance = 0.100E-15 diag: Orthogonalization factor = 0.100E-05 diag: Memory factor = 1.0000 superc: Internal auxiliary supercell: 5 x 5 x 5 = 125 superc: Number of atoms, orbitals, and projectors: 250 3250 2000 ts: ************************************************************** ts: Save H and S matrices = F ts: Save TSHS files in MD/FC simulation = F ts: Save DM and EDM matrices = F ts: Only save the overlap matrix S = F ts: ************************************************************** ************************ Begin: TS CHECKS AND WARNINGS ************************ ************************ End: TS CHECKS AND WARNINGS ************************** ==================================== Single-point calculation ==================================== superc: Internal auxiliary supercell: 5 x 5 x 5 = 125 superc: Number of atoms, orbitals, and projectors: 250 3250 2000 outcell: Unit cell vectors (Ang): 0.000000 1.783500 1.783500 1.783500 0.000000 1.783500 1.783500 1.783500 0.000000 outcell: Cell vector modules (Ang) : 2.522250 2.522250 2.522250 outcell: Cell angles (23,13,12) (deg): 60.0000 60.0000 60.0000 outcell: Cell volume (Ang**3) : 11.3462 refcount: 1> new_DM -- step: 1 Initializing Density Matrix... DM filled with atomic data: refcount: 1> No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 44 443 InitMesh: MESH = 24 x 24 x 24 = 13824 InitMesh: Mesh cutoff (required, used) = 320.000 375.353 Ry New grid distribution [1]: sub = 2 stepf: Methfessel-Paxton step function Using Hermite-Gauss polynomials of order 1 siesta: Program's energy decomposition (eV): siesta: Ebs = -118.490002 siesta: Eions = 564.323437 siesta: Ena = 150.085033 siesta: Ekin = 228.339916 siesta: Enl = -12.247917 siesta: Eso = 0.000000 siesta: Edftu = 0.000000 siesta: DEna = -11.496284 siesta: DUscf = 0.915093 siesta: DUext = 0.000000 siesta: Ex = -103.415496 siesta: Ec = -14.014502 siesta: Exc = -117.429998 siesta: EbV = 0.000000 siesta: eta*DQ = 0.000000 siesta: Emadel = 0.000000 siesta: Emeta = 0.000000 siesta: Emolmec = 0.000000 siesta: Ekinion = 0.000000 siesta: Eharris = -318.683167 siesta: Etot = -326.157594 siesta: FreeEng = -326.157594 iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV) scf: 1 -318.683167 -326.157594 -326.157594 1.067224 -5.701236 0.917221 timer: Routine,Calls,Time,% = IterSCF 1 0.826 26.90 scf: 2 -326.241349 -326.200147 -326.200147 0.007243 -5.504752 0.639878 scf: 3 -326.274979 -326.241237 -326.241237 0.015976 -5.059574 0.007629 scf: 4 -326.241244 -326.241241 -326.241241 0.000249 -5.061884 0.004773 scf: 5 -326.241245 -326.241243 -326.241243 0.000331 -5.063406 0.002070 scf: 6 -326.241245 -326.241244 -326.241244 0.000258 -5.063941 0.001454 scf: 7 -326.241245 -326.241244 -326.241244 0.000176 -5.063965 0.001111 scf: 8 -326.241244 -326.241244 -326.241244 0.000065 -5.063756 0.000786 scf: 9 -326.241244 -326.241244 -326.241244 0.000015 -5.063525 0.000502 scf: 10 -326.241244 -326.241244 -326.241244 0.000013 -5.063369 0.000341 scf: 11 -326.241244 -326.241244 -326.241244 0.000018 -5.063259 0.000175 scf: 12 -326.241244 -326.241244 -326.241244 0.000016 -5.063210 0.000077 scf: 13 -326.241244 -326.241244 -326.241244 0.000013 -5.063195 0.000071 scf: 14 -326.241244 -326.241244 -326.241244 0.000006 -5.063202 0.000051 scf: 15 -326.241244 -326.241244 -326.241244 0.000002 -5.063215 0.000034 scf: 16 -326.241244 -326.241244 -326.241244 0.000001 -5.063225 0.000023 SCF Convergence by DM criterion max |DM_out - DM_in| : 0.0000006460 max |H_out - H_in| (eV) : 0.0000233713 SCF cycle converged after 16 iterations Using DM_out to compute the final energy and forces No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 44 443 siesta: E_KS(eV) = -326.2412 siesta: E_KS - E_eggbox = -326.2412 siesta: Atomic forces (eV/Ang): ---------------------------------------- Tot -0.000000 -0.000000 0.000000 ---------------------------------------- Max 0.000000 Res 0.000000 sqrt( Sum f_i^2 / 3N ) ---------------------------------------- Max 0.000000 constrained Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -22.29 -22.29 -22.29 0.00 0.00 0.00 (Free)E + p*V (eV/cell) -326.0834 Target enthalpy (eV/cell) -326.2412 siesta: Program's energy decomposition (eV): siesta: Ebs = -119.981824 siesta: Eions = 564.323437 siesta: Ena = 150.085033 siesta: Ekin = 224.616581 siesta: Enl = -11.704458 siesta: Eso = 0.000000 siesta: Edftu = 0.000000 siesta: DEna = -8.761412 siesta: DUscf = 0.666251 siesta: DUext = 0.000000 siesta: Ex = -102.832390 siesta: Ec = -13.987413 siesta: Exc = -116.819803 siesta: EbV = 0.000000 siesta: eta*DQ = 0.000000 siesta: Emadel = 0.000000 siesta: Emeta = 0.000000 siesta: Emolmec = 0.000000 siesta: Ekinion = 0.000000 siesta: Eharris = -326.241244 siesta: Etot = -326.241244 siesta: FreeEng = -326.241244 siesta: Final energy (eV): siesta: Band Struct. = -119.981824 siesta: Kinetic = 224.616581 siesta: Hartree = 24.953322 siesta: Edftu = 0.000000 siesta: Eso = 0.000000 siesta: Ext. field = 0.000000 siesta: Exch. = -102.832390 siesta: Corr. = -13.987413 siesta: Bulk bias = 0.000000 siesta: Exch.-corr. = -116.819803 siesta: Ion-electron = -265.230318 siesta: Ion-ion = -193.761027 siesta: Ekinion = 0.000000 siesta: D3 dispersion = 0.000000 siesta: Total = -326.241244 siesta: Fermi = -5.063225 siesta: Stress tensor (static) (eV/Ang**3): siesta: -0.013911 0.000000 0.000000 siesta: 0.000000 -0.013911 0.000000 siesta: 0.000000 0.000000 -0.013911 siesta: Cell volume = 11.346171 Ang**3 siesta: Pressure (static): siesta: Solid Molecule Units siesta: 0.00015151 0.00015151 Ry/Bohr**3 siesta: 0.01391066 0.01391066 eV/Ang**3 siesta: 22.28733056 22.28733063 kBar Basis Enthalpy Calculation: Basis Pressure for species 1(C) : 0.2000000 GPa Orbital volume contribution = 1.054049 eV (Free)E + p_basis*V_orbitals = -325.187196 eV (Free)Eharris+ p_basis*V_orbitals = -325.187196 eV WARNING: BASIS_ENTHALPY and BASIS_HARRIS_ENTHALPY files are deprecated. They will be removed in future releases. Please use system_label.BASIS_ENTHALPY in your scripts instead. cite: Please indicate the Siesta version in published work: 5.4.2 cite: This calculation has made use of features in the following articles cite: which we encourage you to cite in published work. cite: (Please see "siesta.bib" for a BibTeX file.) Primary SIESTA paper DOI: www.doi.org/10.1088/0953-8984/14/11/302 PSML pseudopotential format DOI: www.doi.org/10.1016/j.cpc.2018.02.011 timer: Elapsed wall time (sec) = 12.367 timer: CPU execution times (sec): Routine Calls Time/call Tot.time % siesta 1 16.561 16.561 100.00 Setup 1 1.150 1.150 6.94 bands 1 0.000 0.000 0.00 KSV_init 1 0.000 0.000 0.00 IterGeom 1 15.399 15.399 92.98 geom_init 1 1.096 1.096 6.62 state_init 1 0.209 0.209 1.26 hsparse 1 0.010 0.010 0.06 overlap 1 0.011 0.011 0.07 Setup_H0 1 0.412 0.412 2.49 naefs 2 0.000 0.000 0.00 dnaefs 1 0.000 0.000 0.00 two-body 1 0.000 0.000 0.00 MolMec 2 0.000 0.000 0.00 kinefsm 2 0.011 0.023 0.14 nlefsm 2 0.063 0.127 0.76 DHSCF_Init 1 0.356 0.356 2.15 DHSCF1 1 0.015 0.015 0.09 InitMesh 1 0.015 0.015 0.09 INITMESH 1 0.000 0.000 0.00 DHSCF2 1 0.341 0.341 2.06 REMESH 1 0.048 0.048 0.29 REORD 51 0.000 0.001 0.01 PHION 1 0.265 0.265 1.60 COMM_BSC 75 0.000 0.001 0.01 POISON 19 0.000 0.006 0.04 fft 38 0.000 0.004 0.02 setup_H 17 0.512 8.699 52.52 DHSCF 18 0.568 10.232 61.78 DHSCF3 18 0.508 9.150 55.25 rhoofd 18 0.321 5.770 34.84 XC 18 0.002 0.033 0.20 GXC-CellXC 18 0.002 0.032 0.20 gridxc@cellXC 18 0.002 0.032 0.19 vmat 18 0.185 3.337 20.15 IterSCF 16 0.791 12.655 76.42 compute_dm 16 0.276 4.410 26.63 diagon 16 0.276 4.408 26.62 c-eigval 704 0.002 1.508 9.10 c-buildHS 704 0.002 1.414 8.54 cdiag 1408 0.000 0.241 1.45 cdiag1 1408 0.000 0.011 0.07 cdiag2 1408 0.000 0.048 0.29 cdiag3 1408 0.000 0.155 0.94 c-eigvec 704 0.002 1.581 9.55 cdiag4 704 0.000 0.004 0.02 c-buildD 704 0.002 1.305 7.88 MIXER 15 0.000 0.004 0.03 PostSCF 1 1.648 1.648 9.95 FINAL_HF 1 1.648 1.648 9.95 DHSCF4 1 1.082 1.082 6.53 dfscf 1 1.053 1.053 6.36 overfsm 1 0.012 0.012 0.07 writeHSX 1 0.001 0.001 0.01 state_analysis 1 0.000 0.000 0.00 siesta_move 1 0.000 0.000 0.00 Analysis 1 0.001 0.001 0.01 optical 1 0.000 0.000 0.00 >> End of run: 31-JAN-2026 22:37:53 Job completed Job completed